Accurate prediction of protein relative solvent accessibility using a balanced model
نویسندگان
چکیده
منابع مشابه
Accurate prediction of solvent accessibility using neural networks-based regression.
Accurate prediction of relative solvent accessibilities (RSAs) of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation. Toward that goal we developed a novel method for improved prediction of RSAs. Contrary to other machine learning-based methods from the literature, we do not impose a classification problem with arbitrary boundaries b...
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A Support Vector Machine learning system has been trained to predict protein solvent accessibility from the primary structure. Different kernel functions and sliding window sizes have been explored to find how they affect the prediction performance. Using a cut-off threshold of 15% that splits the dataset evenly (an equal number of exposed and buried residues), this method was able to achieve a...
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Protein domains are considered the basic unit of protein tertiary structure. We have developed a 1D-Recursive Neural Network (1D-RNN) called DOMpro that predicts protein domains using a combination of evolutionary information in the form of profiles and predicted secondary structure and relative solvent accessibility. DOMpro is trained and tested on a curated dataset derived from the CATH datab...
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Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding and protein structure and in scoring remote homology searches. We develop ensembles of bidirectional recurrent neural network architectures to improve the state of the art in both contact and accessibility prediction, leveragi...
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Information on relative solvent accessibility (RSA) of amino acid residues in proteins provides valuable clues to the prediction of protein structure and function. A two-stage approach with support vector machines (SVMs) is proposed, where an SVM predictor is introduced to the output of the single-stage SVM approach to take into account the contextual relationships among solvent accessibilities...
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ژورنال
عنوان ژورنال: BioData Mining
سال: 2017
ISSN: 1756-0381
DOI: 10.1186/s13040-016-0121-5